Tcl, minimization and MD (Warning: I am a lazy ignorant)

From: Edelmiro Moman (moman_at_titus.u-strasbg.fr)
Date: Tue Jun 20 2006 - 10:20:09 CDT

Hello,

I do not know a work of Tcl scripting (or almost any other scripting
language). In consequence, when I try to use a modified version of the
NAMD sample.conf file, I get all kind of warning messages (if I use
constraints, they tell me about bad geometries; otherwise they complain
about high velocities) and the simulation is immediately aborted. I
(ignorant) suspect that NAMD is starting directly with the MD simulation
without doing a previous minimization (as I would wish). This is the
relevant (I guess) fragment of the file:
______________________________________________________________

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
if {0} {
minimize 100
reinitvels $temperature
}

run 50000 ;# 100ps
______________________________________________________________

First silly question: Am I right (by chance)?

Second silly question: What can I do?

Some clues: If the system has been previously minimized the simulation
uses to runs uneventfully; but (!) Autopsfgen removes the hydrogens from
my system and add them again, as a result of which the geometry of the
prolines uses to be completely wrong and that takes me to the original
problem.

Kind regards,

Miro

P.S.: I am not as lazy as I am ignorant. However, as I am aware that my
messages can hurt certain sensibilities, I have include a warning in the
subject so that sensitive people do not have to read them. About
unnecessarily increasing network traffic, I am very sorry about that and
I plan to punish myself as soon as I can think of a suitable way of
doing it.

-- 
Edelmiro Moman
Institut de génétique et de biologie moléculaire et cellulaire
Laboratoire de biologie et de génomique structurales
1, rue Laurent Fries
F-67404 Illkirch Cedex
FRANCE
Tél. : +33 (0)3 88 65 3309 or 3310
Fax : +33 (0)3 88 65 32 76
momanATigbmcDOTu-strasbgDOTfr

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